Contacts of the strand formed by residues 10 - 18 (chain A) in PDB entry 2P3Z
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LYS* 1.3 74.7 - - - +
11A LYS* 1.3 62.0 + - - +
12A HIS 3.8 11.9 - - - +
74A VAL* 3.2 31.0 - - + -
75A GLU 3.5 7.6 - - - +
76A ALA* 4.1 1.3 - - - +
77A GLU* 5.5 0.2 - - - -
104A ILE* 3.8 30.1 - - + +
105A GLU* 4.6 2.0 - - - -
106A GLY* 2.8 28.4 + - - -
107A LYS 2.8 15.4 + - - +
108A CYS 3.9 13.9 - - - +
109A VAL* 3.9 19.7 - - + -
115A ILE* 3.9 10.1 - - + -
144A LEU* 3.5 31.0 - - + -
147A LEU* 4.3 0.7 - - + -
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Residues in contact with LYS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LYS 3.6 1.6 + - - -
10A ILE* 1.3 74.0 - - - +
12A HIS* 1.3 98.1 + - + +
75A GLU* 2.6 20.1 + - - +
76A ALA 3.9 4.0 - - - +
77A GLU* 3.8 32.8 - - + +
79A ARG* 6.2 1.6 - - + -
105A GLU* 3.5 17.9 - - - +
106A GLY 5.0 0.2 + - - -
406A GLU* 4.7 0.7 - - - +
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Residues in contact with HIS 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 3.8 4.7 - - - +
11A LYS* 1.3 129.6 + - + +
13A VAL* 1.3 61.3 + - - +
14A ARG* 3.6 32.9 + - + +
73A GLU 4.1 0.6 - - - +
74A VAL* 3.4 2.3 - - - -
75A GLU* 2.7 55.1 + - + +
105A GLU* 3.6 8.1 - - - +
406A GLU* 3.5 31.6 + - - +
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Residues in contact with VAL 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A HIS* 1.3 75.4 - - - +
14A ARG* 1.3 68.7 + - - +
72A VAL* 3.8 17.7 - - + -
73A GLU 3.4 10.5 - - - +
74A VAL* 3.7 16.8 - - + -
96A VAL* 3.8 19.7 - - + -
97A GLU* 4.2 0.3 - - - +
101A ASN* 3.7 35.9 - - + -
104A ILE* 4.1 23.1 - - + -
105A GLU* 3.1 14.5 + - - +
405A HIS* 3.2 20.9 - - + -
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Residues in contact with ARG 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A HIS* 3.6 28.1 + - + +
13A VAL* 1.3 81.3 - - - +
15A ALA* 1.3 61.2 + - - +
16A TRP* 3.6 28.8 - - + -
72A VAL* 3.4 3.5 - - - -
73A GLU* 2.9 51.3 + - - +
75A GLU* 2.3 46.3 + - - +
96A VAL* 4.9 0.7 - - - -
97A GLU* 3.6 6.1 - - - -
401A ARG* 3.5 35.3 - - - +
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 1.3 75.8 - - - +
16A TRP* 1.3 63.1 + - - +
70A LEU* 3.9 8.3 - - + -
71A ILE 3.1 9.4 - - - +
72A VAL* 4.7 1.1 - - + -
93A CYS* 3.6 35.8 - - + +
96A VAL* 4.1 17.0 - - + -
97A GLU* 3.0 14.6 + - + +
401A ARG* 3.5 21.5 - - - +
402A PRO* 4.5 0.5 - - - +
403A TYR 4.7 0.9 - - - +
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Residues in contact with TRP 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 3.6 41.1 - - + -
15A ALA* 1.3 75.7 - - - +
17A PHE* 1.3 63.0 + - - +
70A LEU* 3.7 1.6 - - - +
71A ILE* 2.8 50.5 + - + +
73A GLU* 3.7 40.4 - - + -
93A CYS* 3.4 13.3 - - - -
393A LEU* 5.0 3.1 - - + -
395A ARG* 5.1 8.1 - - - -
399A LEU* 3.7 41.3 - - + +
400A LYS 3.1 28.5 - - - +
401A ARG* 3.6 24.0 - - + +
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Residues in contact with PHE 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TRP* 1.3 75.8 - - - +
18A ILE* 1.3 72.0 + - - +
19A GLY 3.5 20.9 - - - -
22A THR* 3.3 32.1 - - - -
23A ALA* 3.7 15.0 - - + -
67A LEU 5.6 0.4 - - - -
69A THR 3.0 15.0 - - - +
71A ILE* 4.4 1.1 - - - -
89A GLY* 3.5 19.1 - - - +
90A GLU* 3.4 34.5 - - + -
93A CYS* 4.2 0.7 - - - -
398A HIS 4.1 0.9 - - - +
399A LEU* 3.7 0.2 - - - -
400A LYS* 3.0 51.8 + - + +
402A PRO* 3.6 29.8 - - + -
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Residues in contact with ILE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 1.3 84.2 - - - +
19A GLY* 1.3 67.3 + - - +
23A ALA* 5.1 1.3 - - - -
27A ALA* 3.9 26.2 - - + +
29A GLY* 4.7 2.5 - - - -
34A ASP* 4.7 0.2 - - - +
68A GLY* 3.7 0.2 - - - -
69A THR* 2.9 54.4 + - + +
71A ILE* 3.9 7.0 - - + -
366A PRO* 5.1 1.6 - - + -
367A ILE* 4.0 27.4 - - + -
397A CYS* 4.4 12.6 - - + -
398A HIS 4.0 10.1 - - - +
399A LEU* 3.6 34.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il